An integrated system for real-time polymerase chain reactions (PCR) is available from Cepheid under the brand name GeneXpert™. This system can automate sample preparation and perform steps for DNA extraction in a special cartridge that is coupled to the system. The cartridge includes a thin, diamond-shaped reaction vessel. The side walls of the reaction vessel provide optical windows for optically interrogating the content contained in the reaction vessel. The system includes optical excitation and detection assemblies and two opposing heating plates for heating the reaction vessel when the reaction vessel is received between the heating plates. A fan is provided in the system for cooling the heating plates. The system can perform heating and cooling cycles required for real time PCR and detect the presence of multiple target nucleic acids in the same cartridge.